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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 0
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ), 'gf_id' => 'HOM05D001560', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001560' ), 'data_identifier' => 'HOM05D001560', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001560', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '409', 'num_species' => '76' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Aa31csc239G40' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1486' => 'aag', 'Actinidia34853' => 'ach', 'Actinidia34872' => 'ach', 'Ah.01g011700' => 'amhyb', 'Ah.01g011760' => 'amhyb', 'Ah.02g118870' => 'amhyb', 'Ah.08g210720' => 'amhyb', 'Ah.10g027950' => 'amhyb', 'Ah.10g028090' => 'amhyb', 'Ah.10g028460' => 'amhyb', 'Ah.10g028660' => 'amhyb', 'AL3G44410' => 'aly', 'arahy.Tifrunner.gnm1.ann1.11DKXG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7G246T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4X7TI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HAH5KR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JTWL6Q' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K9CWE8' => 'arhy', 'ATMG00070' => 'ath', 'ATMG00520' => 'ath', 'ATR0693G347' => 'atr', 'AUR62038665' => 'cqu', 'AUR62042344' => 'cqu', 'AUR62042345' => 'cqu', 'BcaC01g01473' => 'bca', 'BcaC09g49590' => 'bca', 'BcaC09g49591' => 'bca', 'BolC1t03442H' => 'bol', 'BolSC28t60305H' => 'bol', 'BolSC28t60329H' => 'bol', 'BolSC28t60362H' => 'bol', 'BolSC28t60405H' => 'bol', 'BolSC28t60433H' => 'bol', 'BraSC177t45760Z' => 'bra', 'BraSC48t46227Z' => 'bra', 'BraSC48t46281Z' => 'bra', 'BraSC48t46315Z' => 'bra', 'BraSC48t46349Z' => 'bra', 'BraSC54t46360Z' => 'bra', 'BraSC77t46636Z' => 'bra', 'BraSC77t46661Z' => 'bra', 'C01p34750' => 'bna', 'C01p34850' => 'bna', 'C01p34990' => 'bna', 'C03p92380' => 'bna', 'C08p30370' => 'bna', 'CAN.G1180.6' => 'can', 'CAN.G1321.15' => 'can', 'CAN.G134.23' => 'can', 'CAN.G223.15' => 'can', 'CAN.G261.14' => 'can', 'CAN.G497.19' => 'can', 'CAN.G505.5' => 'can', 'CAN.G623.2' => 'can', 'CAN.G745.35' => 'can', 'CAN.G85.15' => 'can', 'CAN.G85.16' => 'can', 'CANSAT16G0009' => 'cansat', 'CANSAT16G0039' => 'cansat', 'CARHR282620' => 'chi', 'CARHR282880' => 'chi', 'CARHR287160' => 'chi', 'CARHR287190' => 'chi', 'Ca_14832_v3' => 'car', 'Ca_14833_v3' => 'car', 'Ca_22164_v3' => 'car', 'Ca_22165_v3' => 'car', 'Ca_22175_v3' => 'car', 'Ca_22176_v3' => 'car', 'CDE02G0303' => 'cde', 'CDE02G0735' => 'cde', 'CDE02G2746' => 'cde', 'Cfa023000' => 'cfa', 'ClCG04G001510' => 'cla', 'ClCG06G008570' => 'cla', 'ClCG10G004690' => 'cla', 'ClCG10G004710' => 'cla', 'COL.COLO4_04089' => 'col', 'Cpa.g.sc38.8' => 'cpa', 'Cpa.g.sc89.22' => 'cpa', 'Cre07.g327400' => 'cre', 'CsaV3_1G026590' => 'csa', 'CsaV3_5G015880' => 'csa', 'CsaV3_5G015950' => 'csa', 'CsaV3_UNG210330' => 'csa', 'CsaV3_UNG210420' => 'csa', 'CsaV3_UNG210430' => 'csa', 'CSS0014898' => 'camsi', 'CSS0047048' => 'camsi', 'DCAR_022732' => 'dca', 'DCAR_031657' => 'dca', 'DCAR_032222' => 'dca', 'DCAR_032439' => 'dca', 'DCAR_032442' => 'dca', 'Dinv06677' => 'din', 'Dinv06700' => 'din', 'Dinv29327' => 'din', 'ECA039G0015' => 'eca', 'ECA039G0026' => 'eca', 'ECA041G0003' => 'eca', 'ECA238G3729' => 'eca', 'ECA246G4254' => 'eca', 'EL10Ac7g17432' => 'bvu', 'FvH4_2g28480' => 'fve', 'Gohir.A01G022400' => 'ghi', 'Gohir.A03G134200' => 'ghi', 'Gorai.005G104100' => 'gra', 'GSVIVG01000512001' => 'vvi', 'GSVIVG01006203001' => 'vvi', 'GSVIVG01031611001' => 'vvi', 'HanXRQChr00c0055g0571471' => 'han', 'HanXRQChr01g0012841' => 'han', 'HanXRQChr02g0035261' => 'han', 'HanXRQChr08g0236181' => 'han', 'HanXRQChr08g0236201' => 'han', 'HanXRQChr09g0251121' => 'han', 'HanXRQChr10g0297171' => 'han', 'HanXRQChr10g0297191' => 'han', 'HanXRQChr12g0358671' => 'han', 'HanXRQChr13g0415511' => 'han', 'HanXRQMTg0579631' => 'han', 'HanXRQMTg0579651' => 'han', 'Haze_26224' => 'cav', 'Hma1.2p1_0079F.1_g041900' => 'hma', 'Hma1.2p1_0261F.1_g105120' => 'hma', 'Hma1.2p1_1099F.1_g256790' => 'hma', 'Hund12883' => 'sun', 'Hund12886' => 'sun', 'Hund27586' => 'sun', 'Hund27816' => 'sun', 'Hund27900' => 'sun', 'Hund28069' => 'sun', 'Hund28082' => 'sun', 'Hund28866' => 'sun', 'Hund28883' => 'sun', 'Hund29084' => 'sun', 'Hund29205' => 'sun', 'Hund29341' => 'sun', 'Lalb_Chr00c21g0406061' => 'lal', 'Lalb_Chr00c21g0406161' => 'lal', 'Lalb_Chr00c39g0409051' => 'lal', 'Lalb_Chr00c39g0409121' => 'lal', 'Lalb_Chr00c39g0409231' => 'lal', 'Lalb_Chr00c39g0409261' => 'lal', 'Lalb_Chr00c51g0413141' => 'lal', 'Lalb_Chr00c51g0413181' => 'lal', 'Lj2C1229T3' => 'lonja', 'Lj2P1224T99' => 'lonja', 'Lj2P1227T100' => 'lonja', 'LjContig00315g0001212' => 'lja', 'LjContig00439g0006307' => 'lja', 'LjContig00446g0014136' => 'lja', 'Lsat_1_v5_gn_1_23980' => 'lsa', 'Lsat_1_v5_gn_3_89520' => 'lsa', 'Lsat_1_v5_gn_4_121001' => 'lsa', 'Lsat_1_v5_gn_5_16600' => 'lsa', 'Lsat_1_v5_gn_6_108960' => 'lsa', 'Manes.01G049495' => 'mes', 'Manes.01G049510' => 'mes', 'MapolyY_A0038' => 'mpo', 'MBI05_g23323_MAGBIO' => 'mbi', 'Medtr0212s0080' => 'mtr', 'Medtr4g035695' => 'mtr', 'Medtr4g057110' => 'mtr', 'Medtr8g059730' => 'mtr', 'Migut.D01524' => 'egut', 'Nitab4.5_0000081g0010' => 'nta', 'Nitab4.5_0000172g0630' => 'nta', 'Nitab4.5_0000280g0190' => 'nta', 'Nitab4.5_0000307g0340' => 'nta', 'Nitab4.5_0000307g0350' => 'nta', 'Nitab4.5_0000661g0100' => 'nta', 'Nitab4.5_0000844g0250' => 'nta', 'Nitab4.5_0000886g0180' => 'nta', 'Nitab4.5_0001127g0220' => 'nta', 'Nitab4.5_0001152g0360' => 'nta', 'Nitab4.5_0001152g0390' => 'nta', 'Nitab4.5_0001152g0580' => 'nta', 'Nitab4.5_0001152g0950' => 'nta', 'Nitab4.5_0001152g1040' => 'nta', 'Nitab4.5_0001152g1090' => 'nta', 'Nitab4.5_0001781g0110' => 'nta', 'Nitab4.5_0002739g0100' => 'nta', 'Nitab4.5_0002739g0180' => 'nta', 'Nitab4.5_0008337g0090' => 'nta', 'Nitab4.5_0013170g0020' => 'nta', 'Nitab4.5_0019346g0010' => 'nta', 'Nn1g09975' => 'nnu', 'Nn1g10043' => 'nnu', 'Nn1g10115' => 'nnu', 'Nn4g26006' => 'nnu', 'Nn4g26009' => 'nnu', 'Nn4g26010' => 'nnu', 'Oeu031732.1' => 'oeu', 'Oeu048658.1' => 'oeu', 'Oeu051780.2' => 'oeu', 'Os12g0422971' => 'osa', 'Peaxi162Scf00122g00065' => 'pax', 'Peaxi162Scf00348g00514' => 'pax', 'Peaxi162Scf00348g00515' => 'pax', 'Peaxi162Scf00622g00016' => 'pax', 'Peaxi162Scf00827g00511' => 'pax', 'Peaxi162Scf00931g00038' => 'pax', 'Peaxi162Scf01588g00002' => 'pax', 'PGR028G0023' => 'pgr', 'PGR071G0003' => 'pgr', 'PGSC0003DMG400018984' => 'stu', 'PGSC0003DMG400020882' => 'stu', 'Potri.007G062302' => 'ptr', 'Potri.013G066660' => 'ptr', 'Pp3c13_4900' => 'ppa', 'Pp3c23_18180' => 'ppa', 'Pp3c2_1860' => 'ppa', 'Pp3c2_31660' => 'ppa', 'Prupe.2G039100' => 'ppe', 'Psat1g001600' => 'psa', 'Psat7g198960' => 'psa', 'PSO017G6184' => 'pso', 'PSO675G8388' => 'pso', 'RcHm_v2.0_Chr6g0257991' => 'rch', 'RcHm_v2.0_MTg0498881' => 'rch', 'RhsimMtG0004600' => 'rsi', 'RhsimMtG0005500' => 'rsi', 'RhsimMtG0006100' => 'rsi', 'SabraMtG0003700' => 'sbr', 'SabraMtG0007900' => 'sbr', 'SabraMtG0009500' => 'sbr', 'SabraMtG0009600' => 'sbr', 'SalBow1G1852' => 'sbo', 'Sc04g0005570' => 'sci', 'Sc13g0007750' => 'sci', 'Sed0003843' => 'sed', 'Sed0013276' => 'sed', 'Sed0020323' => 'sed', 'SEGI_16710' => 'sgi', 'SEGI_26668' => 'sgi', 'SGA_v2.0_scaffold245G44645' => 'sas', 'SGA_v2.0_scaffold255G45496' => 'sas', 'SGA_v2.0_scaffold255G45499' => 'sas', 'SHI26652' => 'shi', 'SHI27345' => 'shi', 'SHI27346' => 'shi', 'SHI29512' => 'shi', 'SHI33107' => 'shi', 'SHI33931' => 'shi', 'SHI34605' => 'shi', 'SHI34606' => 'shi', 'SHI34631' => 'shi', 'SHI34635' => 'shi', 'SHI34636' => 'shi', 'SHI34995' => 'shi', 'SHI34996' => 'shi', 'SHI34997' => 'shi', 'SHI34998' => 'shi', 'SHI35000' => 'shi', 'SHI35001' => 'shi', 'SHI35188' => 'shi', 'SHI35231' => 'shi', 'SHI35235' => 'shi', 'SHI35288' => 'shi', 'SHI35320' => 'shi', 'SHI35323' => 'shi', 'SHI35327' => 'shi', 'SHI35332' => 'shi', 'SHI35451' => 'shi', 'SHI35452' => 'shi', 'SHI35482' => 'shi', 'SHI36016' => 'shi', 'SHI36081' => 'shi', 'SHI36139' => 'shi', 'SHI36269' => 'shi', 'SHI36270' => 'shi', 'SHI36372' => 'shi', 'SHI36374' => 'shi', 'SHI36375' => 'shi', 'SHI36380' => 'shi', 'SHI36381' => 'shi', 'SHI36570' => 'shi', 'SHI36572' => 'shi', 'SHI36583' => 'shi', 'SHI36584' => 'shi', 'SHI36585' => 'shi', 'SHI36624' => 'shi', 'SHI36625' => 'shi', 'SHI36627' => 'shi', 'SHI36773' => 'shi', 'SHI36775' => 'shi', 'SHI36784' => 'shi', 'SHI36786' => 'shi', 'SHI36939' => 'shi', 'SHI36971' => 'shi', 'SHI36973' => 'shi', 'SHI37067' => 'shi', 'SHI37068' => 'shi', 'SHI37085' => 'shi', 'SHI37087' => 'shi', 'SHI37134' => 'shi', 'SHI37136' => 'shi', 'SHI37162' => 'shi', 'SHI37164' => 'shi', 'SHI37166' => 'shi', 'SHI37381' => 'shi', 'SHI37382' => 'shi', 'SHI37854' => 'shi', 'SHI37855' => 'shi', 'SHI37900' => 'shi', 'SHI38033' => 'shi', 'SHI38034' => 'shi', 'SHI38099' => 'shi', 'SHI38213' => 'shi', 'SHI38214' => 'shi', 'SHI38463' => 'shi', 'SHI38481' => 'shi', 'SHI38532' => 'shi', 'SHI38561' => 'shi', 'SHI38584' => 'shi', 'SHI38843' => 'shi', 'SHI39078' => 'shi', 'SHI39080' => 'shi', 'SHI39096' => 'shi', 'SHI39097' => 'shi', 'SHI39123' => 'shi', 'SHI39754' => 'shi', 'SHI39990' => 'shi', 'SHI40317' => 'shi', 'SHI40902' => 'shi', 'SHI40903' => 'shi', 'SHI40934' => 'shi', 'SHI42054' => 'shi', 'SHI42241' => 'shi', 'SHI43258' => 'shi', 'SHI43451' => 'shi', 'SHI43452' => 'shi', 'SHI43894' => 'shi', 'SHI44092' => 'shi', 'SHI44216' => 'shi', 'SHI44217' => 'shi', 'SHI44330' => 'shi', 'SHI44984' => 'shi', 'SHI45393' => 'shi', 'SHI45394' => 'shi', 'SHI45575' => 'shi', 'SHI46061' => 'shi', 'SHI46062' => 'shi', 'SHI47572' => 'shi', 'SHI48979' => 'shi', 'SHI49196' => 'shi', 'SHI49510' => 'shi', 'SHI49835' => 'shi', 'SHI50380' => 'shi', 'SHI50434' => 'shi', 'SHI50439' => 'shi', 'SHI50746' => 'shi', 'SHI51143' => 'shi', 'SHI51556' => 'shi', 'SHI51797' => 'shi', 'SHI52730' => 'shi', 'SHI53219' => 'shi', 'SHI53284' => 'shi', 'SHI53856' => 'shi', 'SHI54049' => 'shi', 'SHI54579' => 'shi', 'SHI54824' => 'shi', 'SHI54988' => 'shi', 'SMO053G0006' => 'smo', 'Solyc00g019950.1' => 'sly', 'Solyc01g011060.1' => 'sly', 'Solyc01g020470.3' => 'sly', 'Solyc03g013220.1' => 'sly', 'Solyc03g031640.2' => 'sly', 'Solyc03g061560.3' => 'sly', 'Solyc05g018790.1' => 'sly', 'Solyc08g029250.1' => 'sly', 'Solyc08g065620.1' => 'sly', 'Solyc09g056070.1' => 'sly', 'Solyc09g056080.1' => 'sly', 'Solyc09g056310.1' => 'sly', 'Solyc09g056320.1' => 'sly', 'Solyc09g057810.1' => 'sly', 'Solyc09g057820.1' => 'sly', 'Solyc09g057830.1' => 'sly', 'Solyc11g030880.1' => 'sly', 'Solyc11g030890.3' => 'sly', 'Solyc11g030900.1' => 'sly', 'Sopen00g002540' => 'spe', 'Sopen09g021510' => 'spe', 'Sopen11g018210' => 'spe', 'Sopen11g021670' => 'spe', 'Sp3g25870' => 'spa', 'Sp3g25920' => 'spa', 'Thhalv10002997m.g' => 'esa', 'Thhalv10022839m.g' => 'esa', 'TPR.G15690' => 'tpr', 'TPR.G162' => 'tpr', 'TPR.G20383' => 'tpr', 'TPR.G33338' => 'tpr', 'TPR.G33726' => 'tpr', 'TPR.G36290' => 'tpr', 'TPR.G39706' => 'tpr', 'TPR.G40193' => 'tpr', 'TWI75G1342' => 'twi', 'unitig_87.g27957' => 'ugi', 'unitig_87.g28016' => 'ugi', 'Zm00001eb382940' => 'zma', 'Zm00001eb436070' => 'zma', 'Zm00001eb440310' => 'zma', 'Zm00001eb440380' => 'zma', 'Zm00001eb442180' => 'zma' ) $gf_id = 'HOM05D001560' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001560' ) $data_identifier = 'HOM05D001560' $data_type = 'gf_id' $species_gene_counts = array( 'aar' => (int) 1, 'aag' => (int) 1, 'ach' => (int) 2, 'amhyb' => (int) 8, 'aly' => (int) 1, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 1, 'cqu' => (int) 3, 'bca' => (int) 3, 'bol' => (int) 6, 'bra' => (int) 8, 'bna' => (int) 5, 'can' => (int) 11, 'cansat' => (int) 2, 'chi' => (int) 4, 'car' => (int) 6, 'cde' => (int) 3, 'cfa' => (int) 1, 'cla' => (int) 4, 'col' => (int) 1, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 6, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 1, 'fve' => (int) 1, 'ghi' => (int) 2, 'gra' => (int) 1, 'vvi' => (int) 3, 'han' => (int) 12, 'cav' => (int) 1, 'hma' => (int) 3, 'sun' => (int) 12, 'lal' => (int) 8, 'lonja' => (int) 3, 'lja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 2, 'mpo' => (int) 1, 'mbi' => (int) 1, 'mtr' => (int) 4, 'egut' => (int) 1, 'nta' => (int) 21, 'nnu' => (int) 6, 'oeu' => (int) 3, 'osa' => (int) 1, 'pax' => (int) 7, 'pgr' => (int) 2, 'stu' => (int) 2, 'ptr' => (int) 2, 'ppa' => (int) 4, 'ppe' => (int) 1, 'psa' => (int) 2, 'pso' => (int) 2, 'rch' => (int) 2, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 125, 'smo' => (int) 1, 'sly' => (int) 19, 'spe' => (int) 4, 'spa' => (int) 2, 'esa' => (int) 2, 'tpr' => (int) 8, 'twi' => (int) 1, 'ugi' => (int) 2, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb442180' $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